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Merged
Parent: Added segment picking from faces
merged 19 commits into from
Mar 1, 2024
Merged

Feat: Add method and cli to plot time series #307

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e6760b4
wip: add method to plot time series
sanjayankur31 Feb 20, 2024
f4102b9
chore(pynml): add comment about maintaining backwards compatibility
sanjayankur31 Feb 21, 2024
40ae710
feat(data): add function to load data from given LEMS file
sanjayankur31 Feb 21, 2024
fc994de
chore: improve imports
sanjayankur31 Feb 21, 2024
052526f
chore: correct return value, hints
sanjayankur31 Feb 21, 2024
16275d2
feat(plot): add functions to plot time series from LEMS files and dat…
sanjayankur31 Feb 21, 2024
49b9306
feat(plot): add new `pynml-plottimeseries` cli
sanjayankur31 Feb 21, 2024
6fe2e41
chore: update docs, type hints
sanjayankur31 Feb 21, 2024
94afc30
docs: regenerate man pages
sanjayankur31 Feb 21, 2024
df27d57
fix(timeseries): disable offset by default
sanjayankur31 Feb 21, 2024
97f433d
test(time-series): add assertions
sanjayankur31 Feb 22, 2024
8164b98
test(load-data-from-lems): add more assertions
sanjayankur31 Feb 22, 2024
2b149d6
chore: assertEquals -> assertEqual (deprecated in py3.12)
sanjayankur31 Feb 22, 2024
5b32014
test: add for `test_plot_time_series_from_data_file`
sanjayankur31 Feb 22, 2024
1d7db92
test: add for `plot_time_series_from_lems_file`
sanjayankur31 Feb 22, 2024
c7a78d4
test: test all cli tools also
sanjayankur31 Feb 22, 2024
cc024ed
chore: convert to logging, only calculate when needed
sanjayankur31 Feb 22, 2024
0b6ea15
docs: include new sub-modules
sanjayankur31 Feb 22, 2024
5168139
chore(plottimeseries): improve cli argument parsing
sanjayankur31 Feb 23, 2024
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8 changes: 8 additions & 0 deletions docs/source/pyneuroml.plot.rst
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Expand Up @@ -14,6 +14,14 @@ pyneuroml.plot.Plot module
:undoc-members:
:show-inheritance:

pyneuroml.plot.PlotTimeSeries module
--------------------------------

.. automodule:: pyneuroml.plot.PlotTimeSeries
:members:
:undoc-members:
:show-inheritance:

pyneuroml.plot.PlotSpikes module
--------------------------------

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8 changes: 8 additions & 0 deletions docs/source/pyneuroml.utils.rst
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Expand Up @@ -22,6 +22,14 @@ pyneuroml.utils.plot module
:undoc-members:
:show-inheritance:

pyneuroml.utils.misc module
---------------------------

.. automodule:: pyneuroml.utils.misc
:members:
:undoc-members:
:show-inheritance:

pyneuroml.utils.cli module
---------------------------

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10 changes: 6 additions & 4 deletions man/man1/common.h2m
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@@ -1,14 +1,16 @@
[see also]
[see-also]
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
14 changes: 12 additions & 2 deletions man/man1/generate-man-pages.sh
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@@ -1,7 +1,7 @@
#!/bin/bash

# Copyright 2023 Ankur Sinha
# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
# File : generate-man-pages.sh
#
# Generate man pages for all pyNeuroML command lines using help2man
Expand All @@ -27,6 +27,17 @@ else
echo ".PP" >> version.h2m
echo "${fullversioninfo}" >> version.h2m

echo "Generating common file: common.h2m"
echo "[see-also]" > common.h2m

for f in ${bin_location}/pynml*
do
current_file=$(basename $f)
echo ".BR ${current_file} (1)," >> common.h2m
done
echo ".PP" >> common.h2m
echo "Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem." >> common.h2m

cat common.h2m version.h2m >> common-temp.h2m

for f in ${bin_location}/pynml*
Expand All @@ -39,4 +50,3 @@ else

rm common-temp.h2m
fi

20 changes: 11 additions & 9 deletions man/man1/pynml-archive.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.0" "User Commands"
.TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.2" "User Commands"
.SH NAME
pynml-archive \- manual page for pynml-archive v1.2.0
pynml-archive \- manual page for pynml-archive v1.2.2
.SH DESCRIPTION
usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
.TP
Expand All @@ -27,20 +27,22 @@ Extension to use for archive.
.TP
\fB\-filelist\fR [<explicit list of files to create archive of> ...]
Explicit list of files to create archive of.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-channelanalysis.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.0" "User Commands"
.TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.2" "User Commands"
.SH NAME
pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.0
pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.2
.SH DESCRIPTION
usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
.TP
Expand Down Expand Up @@ -92,20 +92,22 @@ the plots for the channel
\fB\-ivCurve\fR
Save currents through voltage clamp at each level &
plot current vs voltage for ion channel
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-channelml2nml.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.0" "User Commands"
.TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.2" "User Commands"
.SH NAME
pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.0
pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.2
.SH DESCRIPTION
usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
.TP
Expand All @@ -23,20 +23,22 @@ Path to the XSLT file
.TP
\fB\-saveToFile\fR <Output file name>
Name of the outputfile file
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-modchananalysis.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.0" "User Commands"
.TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.2" "User Commands"
.SH NAME
pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.0
pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.2
.SH DESCRIPTION
usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
.TP
Expand Down Expand Up @@ -54,20 +54,22 @@ in mM)
.TP
\fB\-modFile\fR <name of mod file>
Name of the mod file containing the channel
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-plotchan.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.0" "User Commands"
.TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.2" "User Commands"
.SH NAME
pynml-plotchan \- manual page for pynml-plotchan v1.2.0
pynml-plotchan \- manual page for pynml-plotchan v1.2.2
.SH DESCRIPTION
usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
.IP
Expand All @@ -23,20 +23,22 @@ Do not generate distance plots
.TP
\fB\-nogui\fR
Do not show plots as they are generated
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-plotmorph.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.0" "User Commands"
.TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.2" "User Commands"
.SH NAME
pynml-plotmorph \- manual page for pynml-plotmorph v1.2.0
pynml-plotmorph \- manual page for pynml-plotmorph v1.2.2
.SH DESCRIPTION
usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
.TP
Expand Down Expand Up @@ -53,20 +53,22 @@ Name of the image file, for 2D plot
\fB\-square\fR
Scale axes so that image is approximately square, for
2D plot
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
20 changes: 11 additions & 9 deletions man/man1/pynml-plotspikes.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
.TH PYNML-PLOTSPIKES "1" "February 2024" "pynml-plotspikes v1.2.0" "User Commands"
.TH PYNML-PLOTSPIKES "1" "February 2024" "pynml-plotspikes v1.2.2" "User Commands"
.SH NAME
pynml-plotspikes \- manual page for pynml-plotspikes v1.2.0
pynml-plotspikes \- manual page for pynml-plotspikes v1.2.2
.SH DESCRIPTION
usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
.TP
Expand Down Expand Up @@ -42,20 +42,22 @@ Window for rate calculation in ms
.TP
\fB\-rateBins\fR <rate bins>
Number of bins for rate histogram
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
.SH "SEE ALSO"
.SH "SEE-ALSO"
.BR pynml (1),
.BR pynml-archive (1),
.BR pynml-channelanalysis (1),
.BR pynml-channelml2nml (1),
.BR pynml-modchananalysis (1),
.BR pynml-plotchan (1),
.BR pynml-plotspikes (1),
.BR pynml-plotmorph (1),
.BR pynml-modchannelanalysis (1),
.BR pynml-plotspikes (1),
.BR pynml-plottimeseries (1),
.BR pynml-povray (1),
.BR pynml-sonata (1),
.BR pynml-summary (1),
.BR pynml-tune (1).
.BR pynml-tune (1),
.PP
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
.SH ENVIRONMENT
.PP
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
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